When an Order is either created in the Point of Sale or from your Website and has been Accepted, the Credit Card Transaction on the Order is captured and the Order has no Balance. If the Order is then Canceled, you need to manually refund the Customer's Credit Card.
Step 1) Cancel the Order. A Return will automatically be created for the amount of the Order, and a Credit Memo will automatically be created to keep the Order balanced.
Step 2) Click on the Credit Memo that was created to issue the Refund back to the Customer.
Step 3) Click the Action Button (+) in the Transaction Table when viewing the Credit Memo to issue payment against the Credit Memo. Select Credit Card and input the amount you wish to refund from the initial transaction. Hit Apply.